Impact of Interleukin 10 Deficiency on Intestinal Epithelium Responses to Inflammatory Signals.

Interleukin 10 (IL-10) is a pleiotropic, anti-inflammatory cytokine that has a major protective role in the intestine. Although its production by cells of the innate and adaptive immune system has been extensively studied, its intrinsic role in intestinal epithelial cells is poorly understood. In this study, we utilised both ATAC sequencing and RNA sequencing to define the transcriptional response of murine enteroids to tumour necrosis factor (TNF). We identified that the key early phase drivers of the transcriptional response to TNF within intestinal epithelium were NFκB transcription factor dependent. Using wild-type and Il10-/- enteroid cultures, we showed an intrinsic, intestinal epithelium specific effect of IL-10 deficiency on TNF-induced gene transcription, with significant downregulation of identified NFκB target genes Tnf, Ccl20, and Cxcl10, and delayed overexpression of NFκB inhibitor encoding genes, Nfkbia and Tnfaip3. IL-10 deficiency, or immunoblockade of IL-10 receptor, impacted on TNF-induced endogenous NFκB activity and downstream NFκB target gene transcription. Intestinal epithelium-derived IL-10 appears to play a crucial role as a positive regulator of the canonical NFκB pathway, contributing to maintenance of intestinal homeostasis. This is particularly important in the context of an inflammatory environment and highlights the potential for future tissue-targeted IL-10 therapeutic intervention.

The Antibiotic Dosage of Fastest Resistance Evolution: Gene Amplifications Underpinning the Inverted-U.

To determine the dosage at which antibiotic resistance evolution is most rapid, we treated Escherichia coli in vitro, deploying the antibiotic erythromycin at dosages ranging from zero to high. Adaptation was fastest just below erythromycin's minimal inhibitory concentration (MIC) and genotype-phenotype correlations determined from whole genome sequencing revealed the molecular basis: simultaneous selection for copy number variation in three resistance mechanisms which exhibited an "inverted-U" pattern of dose-dependence, as did several insertion sequences and an integron. Many genes did not conform to this pattern, however, reflecting changes in selection as dose increased: putative media adaptation polymorphisms at zero antibiotic dosage gave way to drug target (ribosomal RNA operon) amplification at mid dosages whereas prophage-mediated drug efflux amplifications dominated at the highest dosages. All treatments exhibited E. coli increases in the copy number of efflux operons acrAB and emrE at rates that correlated with increases in population density. For strains where the inverted-U was no longer observed following the genetic manipulation of acrAB, it could be recovered by prolonging the antibiotic treatment at subMIC dosages.

Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis.

Defining the contributions and interactions of paternal and maternal genomes during embryo development is critical to understand the fundamental processes involved in hybrid vigor, hybrid sterility, and reproductive isolation. To determine the parental contributions and their regulation during Arabidopsis embryogenesis, we combined deep-sequencing-based RNA profiling and genetic analyses. At the 2-4 cell stage there is a strong, genome-wide dominance of maternal transcripts, although transcripts are contributed by both parental genomes. At the globular stage the relative paternal contribution is higher, largely due to a gradual activation of the paternal genome. We identified two antagonistic maternal pathways that control these parental contributions. Paternal alleles are initially downregulated by the chromatin siRNA pathway, linked to DNA and histone methylation, whereas transcriptional activation requires maternal activity of the histone chaperone complex CAF1. Our results define maternal epigenetic pathways controlling the parental contributions in plant embryos, which are distinct from those regulating genomic imprinting.

Genetic variants in matrix metalloproteinase genes are associated with development of gastric ulcer in H. Pylori infection.

BACKGROUND AND AIMS: Matrix metalloproteinases (MMPs) are a family of enzymes that degrade most of the macromolecules making up the extracellular matrix. H. pylori infection increases the secretion of MMPs in the gastric mucosa leading to severe mucosal damage. The aim of this study was to investigate if genetic variants in MMPs involved in the inflammatory response to H. pylori could predispose patients with chronic H. pylori infection to develop gastric ulcer disease. METHODS: A total of 599 H. pylori-infected patients undergoing gastroscopy were genotyped for 20 SNPs covering the MMP-1, -3, -7, and -9 genes by TaqMan technology. Haplotype and single marker analysis was conducted to assess associations with gastric ulcer disease. RESULTS: Carriage of allele G of the functional promoter variant MMP-7-181 was significantly associated with gastric ulcer conferring a 1.6-fold increased risk (95% CI: 1.0-2.6, p = 0.037). In addition, carriage of allele A of a coding SNP in exon 6 of MMP-9 confers a 2.4-fold increased risk (95% CI: 1.0-2.6, p = 0.013) for gastric ulcer. CONCLUSION: The level of association found in this study is in agreement with the nature of a complex genetic disease. Genetic variations in the MMP-7 and -9 gene may be part of a complex genetic risk profile to develop gastric ulcer in chronic H. pylori infection. Further studies are warranted to elucidate the pathophysiological role of these genes in ulcerogenesis.

Germline variations of the topoisomerase IIalpha gene as risk factors for primary gastric B-cell lymphoma.

We investigated if germline variations of the Topoisomerase II alpha gene could predispose patients with chronic Helicobacter pylori infection to develop gastric lymphoma and conducted a mutation detection of the entire promoter region. Single marker and haplotype analysis did not reveal any associations with development of gastric lymphoma in general, histological grade or stage of disease (P>0.05). No genetic variations in the promotor region were found in 92 chromosomes of lymphoma patients and controls and linkage disequilibrium indicated a highly conserved genomic region. The results of our work exclude genetic variations as predisposing factors of primary gastric B-cell lymphoma development.

Life-threatening chronic enteritis due to colonization of the small bowel with Stenotrophomonas maltophilia.

Chronic diarrheal illness and malabsorption are challenging diagnostic and clinical problems. The identification of the causative pathogens that are involved in gastrointestinal infections is often difficult. It took 85 years after the first description of a case of intestinal lipodystrophy by Georg Whipple in 1907 until the causative bacterium was characterized by using molecular genetics techniques. We here report the complicated clinical course of a young patient with chronic diarrhea accompanied by severe, life-threatening malabsorption with extensive weight loss. Histology and glucose hydrogen breath test were suggestive of a bacterial overgrowth syndrome in the small bowel, but standard culture-based techniques and serology failed to identify the causative bacteria. Thus, bacterial ribosomal DNA (16S ribosomal DNA) was extracted from duodenal biopsy samples and analyzed by community fingerprinting and species-specific polymerase chain reaction. Stenotrophomonas maltophilia was identified as the cause of chronic infectious enteritis. Only specific long-term antibiotic treatment with co-trimoxazole had a durable clinical effect and led to normalization of 16S ribosomal DNA profiles. This case shows the role of rare and uncommon bacteria in refractory and chronic human gastrointestinal infections. Genomic techniques, including 16S-based single-strand conformation polymorphism analysis, will play an increasing role in the diagnosis of chronic infections with facultatively pathogenic bacteria or in the clinical analysis of complex bacterial communities such as the intestinal bacterial microflora. Future enhancements in detection techniques will show that chronic bacterial infections are more frequent as a cause of gastrointestinal malfunction than commonly thought.